DOI: 10.18129/B9.bioc.doubletrouble  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see doubletrouble.

Identification and classification of duplicated genes

Bioconductor version: 3.17

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are: i. whole-genome duplication (WGD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). If users want a simpler classification scheme, duplicates can also be classified into WGD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Author: Fabrício Almeida-Silva [aut, cre] , Yves Van de Peer [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at>

Citation (from within R, enter citation("doubletrouble")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Identification and classification of duplicated genes
PDF   Reference Manual
Text   NEWS


biocViews ComparativeGenomics, FunctionalGenomics, Network, Phylogenetics, Software, WholeGenome
Version 1.0.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License GPL-3
Depends R (>= 4.2.0)
Imports syntenet, GenomicRanges, Biostrings, mclust, MSA2dist(>= 1.1.5), ggplot2, stats, utils
Suggests testthat (>= 3.0.0), knitr, feature, BiocStyle, rmarkdown, covr, sessioninfo
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package doubletrouble_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) doubletrouble_1.0.0.tgz
macOS Binary (arm64) doubletrouble_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: